When a genetic analyzer is used to determine the base sequence of DNA, four time-series measured data sets corresponding to four kinds of bases, A (adenine), G (guanine), C (cytosine), and T (thymine) are obtained. According to a conventional method such as Phred (see Non-Patent Document 1), such measured data sets are subjected to processing such as noise elimination and mobility correction for correcting a time lag among time-series data sets resulting from a difference in migration speed among different labeling dyes depending on the kind of base to obtain “analytical data”. Then, a nucleic acid base sequence is determined based on the “analytical data”, and the degree of reliability of the nucleic acid base sequence is determined by analyzing the characteristic indicators of the “analytical data”.
Such a conventional method such as Phred uses, as the characteristic indicators of “analytical data”, variations in peak-to-peak intervals, the ratio of the amplitude of a peak having been identified as a nucleic acid base peak to a noise peak, and the distance to a part having an unresolved base. The reliability degree value of each base is assessed by evaluating the measured values of these characteristic indicators in combination. This is based on the findings that highly-reliable “analytical data” is characterized in that peaks are spaced at regular intervals, the ratio of the amplitude of a peak having been identified as a nucleic acid base peak to a noise peak is high, and a part having an unresolved base is not near a peak having been identified as a nucleic acid base peak.
The reliability degree value of each base is referred to as a quality value (hereinafter, sometimes abbreviated as “QV”), and is defined by the following formula (1):QV=−10×Log10(Err)where Err is an error probability  (1)
Further, in the case of the conventional method such as Phred, in order to comprehensively evaluate two or more characteristic indicators, statistical data is previously prepared by mapping actual error rates onto parametric space defined by the characteristic indicators. The actual error rates are obtained in such a manner that the base sequences of many samples having known base sequences are determined by measurement and checked against the correct base sequences of these samples. The degree of reliability of a base sequence determined by analyzing measured data is assessed using the formula (1) by reference to the statistical data.
More specifically, an error probability Err (i, j, k) is measured by statistically processing many bases having parameters (Ai, Bj, Ck). In a case where an identified base of an unknown sample has parameters (Ai, Bj, Ck), QV of the base is determined by the formula (1).    Non-Patent Document 1: Ewing B, Green P, Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Research 8, pp. 186-194, 1998    Non-Patent Document 2: S. Minami, “Waveform data processing for scientific measurement”, CQ publishing, pp. 111-113 and pp. 186-191, 1986    Patent Document 1: Japanese Patent Application Laid-open No. 2002-168868    Patent Document 2: Japanese Patent Application Laid-open No. 2002-228633